[Pw_forum] Effective parallel implementation?

Pascal Boulet pascal.boulet at univ-amu.fr
Tue Sep 1 22:03:49 CEST 2015 

Hello Bang,

For comparison, in my case I have been able to run a vc-relax job on 92 atoms, 48 cores in 12 hours. I am using USPP, gamma point calculation and no symmetry. This is a slab. I am using a basic command line: mpirun -np 40 pw.x < input > output.  

Of course, I do not know if our computers are comparable, but it seems that your performance could be improved, probably through compilation optimization. I am using national supercomputer facility and QE was installed by a system manager, so I cannot give compilation details.

I have noted a few things in your input that I (personally) would change:
Energy convergence=1d-7
Force convergence=1d-4 eventually 1d-5 if you plan to compute phonons (in any case it should not be smaller than energy convergence)
conv_thr=1d-8 (or smaller — 1d-9, 1d-10 -- in case of phonon calculations only)
It seems that your are using USPP, so in this case I think you can reduce Ecutwfc to between 30-50, but you have to test this, and Ecutrho should be between 8 and 12 times Ecutwfc.
Check also if you can reduce the number of k-points: your cell seems to be rather large.

HTH
Pascal


Le 1 sept. 2015 à 21:18, Bang C. Huynh <cbh31 at cam.ac.uk> a écrit :

> Dear all,
> 
> I am currently attempting to perform several structural relaxation calculations on supercells that contain at least ~70 atoms (and even more, say hundreds). My calculations are being done on a single node with 40 cores, 2.4 GHz, Intel Xeon E5-2676v3 and 160 GiB memory (m4.10xlarge Amazon EC2). I am just wondering if my implementation for parallelism is 'reasonable' in the sense that the resources are fully utilised, and not in some way underutilised or poorly distributed. I'm pretty new to this so I'm not sure what to expect... Should I be happy with the current performance, can it be better, or should I consider deploying more resources and is it worth it? Currently one scf iteration takes around 5-7 minutes. Scf-convergence is achieved after around 50 scf iterations, and I'm not sure how long it's going to take for the vc-relax iterations to converge...
> 
> The input file is shown below. I use this command to initiate the job:
> 
>> mpirun -np 40 pw.x -npool 2 -ndiag 36 < skutU0.125_vc.vc2 > skutU0.125_vc.vc2.out
>> 
> Thank you for your help.
> 
>  
> Regards,
> 
> -- 
> Bang C. Huynh
> Peterhouse
> University of Cambridge
> CB2 1RD
> The United Kingdom
> 
> ========input=======
> 
>> &CONTROL
>> title = skutterudite-U-doped ,
>> calculation = 'vc-relax' ,
>> outdir = './' ,
>> wfcdir = './' ,
>> pseudo_dir = '../pseudo/' ,
>> prefix = 'skutU0.125_vc' ,
>> etot_conv_thr = 1.0D-5 ,
>> forc_conv_thr = 1.95D-6 ,
>> nstep = 250 ,
>> dt = 150 ,
>> /
>> &SYSTEM
>> ibrav = 6,
>> celldm(1) = 17.06
>> celldm(3) = 2,
>> nat = 66,
>> ntyp = 3,
>> ecutwfc = 93 ,
>> ecutrho = 707 ,
>> occupations = 'smearing' ,
>> starting_spin_angle = .false. ,
>> degauss = 0.02 ,
>> smearing = 'methfessel-paxton' ,
>> /
>> &ELECTRONS
>> conv_thr = 1D-10 ,
>> /
>> &IONS
>> /
>> &CELL
>> cell_dynamics = 'damp-w' ,
>> cell_dofree = 'all' ,
>> /
>> ATOMIC_SPECIES
>> Co 58.93000 Co.pz-nd-rrkjus.UPF 
>> Sb 121.76000 Sb.pz-bhs.UPF 
>> U 238.02891 U.pz-spfn-rrkjus_psl.1.0.0.UPF 
>> ATOMIC_POSITIONS crystal 
>> Co 0.250000000 0.250000000 0.125000000 0 0 0 
>> Co 0.250000000 0.250000000 0.625000000 0 0 0 
>> Co 0.750000000 0.750000000 0.375000000 0 0 0 
>> Co 0.750000000 0.750000000 0.875000000 0 0 0 
>> Co 0.750000000 0.750000000 0.125000000 0 0 0 
>> Co 0.750000000 0.750000000 0.625000000 0 0 0 
>> Co 0.250000000 0.250000000 0.375000000 0 0 0 
>> Co 0.250000000 0.250000000 0.875000000 0 0 0 
>> Co 0.750000000 0.250000000 0.375000000 0 0 0 
>> Co 0.750000000 0.250000000 0.875000000 0 0 0 
>> Co 0.250000000 0.750000000 0.125000000 0 0 0 
>> Co 0.250000000 0.750000000 0.625000000 0 0 0 
>> Co 0.250000000 0.750000000 0.375000000 0 0 0 
>> Co 0.250000000 0.750000000 0.875000000 0 0 0 
>> Co 0.750000000 0.250000000 0.125000000 0 0 0 
>> Co 0.750000000 0.250000000 0.625000000 0 0 0 
>> Sb 0.000000000 0.337592989 0.078553498 
>> Sb 0.000000000 0.337592989 0.578553498 
>> Sb 0.000000000 0.662407041 0.421446502 
>> Sb 0.000000000 0.662407041 0.921446502 
>> Sb 0.000000000 0.662407041 0.078553498 
>> Sb 0.000000000 0.662407041 0.578553498 
>> Sb 0.000000000 0.337592989 0.421446502 
>> Sb 0.000000000 0.337592989 0.921446502 
>> Sb 0.157106996 0.000000000 0.168796495 
>> Sb 0.157106996 0.000000000 0.668796480 
>> Sb 0.842893004 0.000000000 0.331203520 
>> Sb 0.842893004 0.000000000 0.831203520 
>> Sb 0.157106996 0.000000000 0.331203520 
>> Sb 0.157106996 0.000000000 0.831203520 
>> Sb 0.842893004 0.000000000 0.168796495 
>> Sb 0.842893004 0.000000000 0.668796480 
>> Sb 0.337592989 0.157106996 0.000000000 
>> Sb 0.337592989 0.157106996 0.500000000 
>> Sb 0.662407041 0.842893004 0.000000000 
>> Sb 0.662407041 0.842893004 0.500000000 
>> Sb 0.662407041 0.157106996 0.000000000 
>> Sb 0.662407041 0.157106996 0.500000000 
>> Sb 0.337592989 0.842893004 0.000000000 
>> Sb 0.337592989 0.842893004 0.500000000 
>> Sb 0.500000000 0.837592959 0.328553498 
>> Sb 0.500000000 0.837592959 0.828553498 
>> Sb 0.500000000 0.162407011 0.171446502 
>> Sb 0.500000000 0.162407011 0.671446502 
>> Sb 0.500000000 0.162407011 0.328553498 
>> Sb 0.500000000 0.162407011 0.828553498 
>> Sb 0.500000000 0.837592959 0.171446502 
>> Sb 0.500000000 0.837592959 0.671446502 
>> Sb 0.657106996 0.500000000 0.418796480 
>> Sb 0.657106996 0.500000000 0.918796480 
>> Sb 0.342893004 0.500000000 0.081203505 
>> Sb 0.342893004 0.500000000 0.581203520 
>> Sb 0.657106996 0.500000000 0.081203505 
>> Sb 0.657106996 0.500000000 0.581203520 
>> Sb 0.342893004 0.500000000 0.418796480 
>> Sb 0.342893004 0.500000000 0.918796480 
>> Sb 0.837592959 0.657106996 0.250000000 
>> Sb 0.837592959 0.657106996 0.750000000 
>> Sb 0.162407011 0.342893004 0.250000000 
>> Sb 0.162407011 0.342893004 0.750000000 
>> Sb 0.162407011 0.657106996 0.250000000 
>> Sb 0.162407011 0.657106996 0.750000000 
>> Sb 0.837592959 0.342893004 0.250000000 
>> Sb 0.837592959 0.342893004 0.750000000 
>> U 0.000000000 0.000000000 0.000000000 
>> U 0.000000000 0.000000000 0.500000000 
>> K_POINTS automatic 
>> 4 4 2 0 0 0
>> 
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--
Pascal Boulet - MCF HDR, Resp. L1 MPCI - DEPARTEMENT CHIMIE
Aix-Marseille Université - ST JEROME - Avenue Escadrille Normandie Niemen - 13013 Marseille
Tél: +33(0)4 13 55 18 10 - Fax : +33(0)4 13 55 18 50
Site : http://allos.up.univ-mrs.fr/pascal - Email : pascal.boulet at univ-amu.fr
Afin de respecter l'environnement, merci de n'imprimer cet email que si nécessaire.

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